The development of engineered nanomaterials opens tremendous opportunities for their application as therapeutic and diagnostic tools, as well as in the fields of consumer products. As the newly developed material subtype, they exhibit great activities for the high ratio of surface to total atoms. In the bio-system, the activity can render nanomaterials some negative outcomes for their unexpected deposition in organs and cells, the cellular response to the exogenous substance and the interfacial reaction with biomolecules. In this review, we have discussed the evolution of nanotoxicology studies in the past ten years mainly emerging from our laboratory. The early in vivo studies mainly focused on the biokinetic of inhaled nanoparticles and their impacts on mammal tissues, such as the central nervous system, respiratory system, cardiovascular system and so on. Then the scope extended to engineered nanomaterials used as food additives and medicines, as well as their influence on alimentary and reproductive systems. In vitro experiments to study the nanoparticle-cell interaction and nanoparticle-biomolecule interplay are indispensable to reveal the mechanisms behind the macroscopic phenomenon. In addition, novel tools such as new model organisms and synchrotron radiation-based techniques are used to facilitate our understanding of the toxicology profile of nanomaterials.